The characters combine literally to mean “difficulties, layer upon layer” (困难 + 重重). This creates a much stronger and more descriptive image than simply saying something is 很难 (hěn nán - very difficult).
In Chinese culture, there's a strong emphasis on perseverance (坚持 - jiānchí) and enduring hardship. The idiom 困难重重 isn't just a complaint; it often serves as the setup in a story about resilience. It acknowledges the reality that any worthwhile endeavor—be it building a nation, a business, or one's character—will inevitably be filled with challenges. A good Western comparison is the phrase “an uphill battle,” but there's a subtle difference. “Uphill battle” focuses on the strenuous effort required to overcome a single, continuous obstacle (the incline). 困难重重 emphasizes the multiplicity and variety of the problems. It's an uphill battle on a path that is also full of potholes, falling rocks, and confusing forks in the road. It speaks to a situation's complexity and the feeling of being assailed by problems from all sides, a concept deeply understood in a culture with a long history of overcoming immense collective challenges.
困难重重 is a fairly formal and literary idiom. You won't hear it used to describe everyday annoyances.